Assuming you trust Silent Circle (and all their manufacturers and suppliers), then it could be considered secure as it comes in the box (Assuming the box is sealed, and hasn't been tampered with).
As soon as you add any third party software, you have to be sure that you trust the developers of it, and the distributors of it, to the same level. They are able to run software on the device, which might be able to do things which seem required, but actually allow for unintended data to be exfiltrated. For example, if applications can access the motion sensor, they may be able to work out any PIN entry made whilst they are running, even if not currently active. There have been a couple of research investigations into this.
If you don't trust the application to the same level, you are effectively reducing the trust in the whole device to the weakest part. This isn't specific to the Blackphone, but to any device where you introduce software which isn't trusted to the same level.
There isn't any reason to think that installing third party software will definitely compromise the device, just that you should be prepared to perform the same level of due diligence on any software as you are on the device itself.